DBASS5 - Record Details
| Gene |
HMBS (Ensembl) |
Location of Aberrant 5' Splice Site | Intron |
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| Phenotype |
Acute intermittent porphyria (OMIM) |
Distance between Authentic and Aberrant 5' Splice Site (nt) |
+15
|
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| Mutation | IVS7+2T>C | Change in the Reading Frame |
0
|
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| Reference(s) |
Martinez di Montemuros, F., Di Pierro, E., Fargion, S., Biolcati, G., Griso, D., Macri, A., Fiorelli, G. and Cappellini, M.D. (2000) Molecular analysis of the hydroxymethylbilane synthase (HMBS) gene in Italian patients with acute intermittent porphyria: report of four novel mutations. Hum Mutat, 15, 480. Pub Med Article # 10790212 |
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| Nucleotide Sequence[a] | ggctggctgc tcataccctt tctctttgcc cccctctccc atctctatag AGTGGACCTG GTTGTTCACT CCTTGAAGGA CCTGCCCACT GTGCTTCCTC CTGGCTTCAC CATCGGAGCC ATCTGCAAg( t>c)aagagt cttgcaa/gt aaggggcttg ggcaggggta ggcatcatgt gaacctttgc ctttcccttt ggggcctgac cctctgcttc agggttatct cctctgccct gaggagtgtt gactggtggc agaaaactca agaaatacca gtgagttggc aatcgagaga gaatagaggt gatctgaact taaatctctt ccctcattct gtgcccttcc ctcctccccc agGCGGGAAA ACCCTCATGA TGCTGTTGTC TTTCACCCAA AATTTGTTGG GAAGACCCTA GAAACCCTGC CAGAGAAGAG | ||||
| Terminal Exon? | No | ||||
| Splice Site Strength[b] | Authentic Site |
Aberrant Site |
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| Maximum Entropy Model [1] |
7.61
|
7.66
|
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| Maximum Dependence Decomposition Model [2] |
11.08
|
11.98
|
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| First Order Markov Model [1] |
7.43
|
7.38
|
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| Weight Matrix Model [1] |
8.97
|
8.97
|
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| Genomic Co-ordinates (hg38) | |||||
| Aberrant Splice Site |
chr11:119089775/119089776 |
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| Mutation |
chr11:119089762 |
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Legend
- [a] /, cryptic or de novo splice sites; > nucleotide substitutions; (), deletions; [], duplications or insertions. Intronic sequences are in lower case (in blue), exons are in upper case (in green)
- [b] Shapiro and Senapathy matrix scores were calculated according to an algorithm published previously (1). Maximum entropy and the first-order Markov and weight matrix models were computed as described (2)
References
- Shapiro, M.B. and Senapathy, P. (1987) RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res., 15, 7155-7174.
- Yeo, G. and Burge, C.B. (2004) Maximum entropy modelling of short sequence motifs with applications to RNA splicing signals. J. Comput. Biol., 11, 377-394.
- Burge, C. 1998. Modeling dependencies in pre-mRNA splicing signals. In Computational methods in molecular biology (eds. S.L. Salzberg et al.), chapter 8, pp. 129–164. Elsevier Science, Philadelphia, PA.